Summary

DIA-NN Experiments

DIA-NN Experiments

default_1 F:/GW/raw_data/wGW027.raw

default_2 F:/GW/raw_data/wGW028.raw

default_3 F:/GW/raw_data/wGW029.raw

Ion Sampling

Channel wise MS1 Intensity for Precursors

Plotting the MS1 intensity for all precursors which were associated with one of the defined channels.

Precursors Identified across Gradient

Precursor are plotted across the chromatographic gradient.

MS1 Intensity summed over all Channels.

Plotting the MS1 intensity for all precursors summed over all channels.

MS1 Intensity for Intersected Precursors, summed over all Channels.

Plotting the MS1 intensity for all precursors summed over all channels. Only intersected precursors present in all loaded experiments are shown.

Normalized MS1 Intensity for Intersected Precursors

Plotting the MS1 Intensity for intersected precursors summed over all channels. Experiments are normalized to the first experiment.

Number of Precursors by Charge State

Number of precursors observed during MS1 scans by charge state

Ms1 Fill Time Distribution

Ms1 fill times along gradient

Ms1 Fill Times along Gradient

The averge fill time is shown in magenta for different bins along the retention time gradient. The standard deviation is depicted as area in blue, scans outside this area are shown as single datapoints.

Ms1 total Ion Current along Gradient

The toal Ion Current (TIC) is shown for bins along the retention time gradient.

Ms2 Fill Time Distribution

Ms2 fill times along gradient

Ms2 Fill Times along Gradient

The averge fill time is shown in magenta for different bins along the retention time gradient. The standard deviation is depicted as area in blue, scans outside this area are shown as single datapoints.

Ms2 Fill Time Matrix

The average Ms2 fill times are shown across the gradient for every distinct Ms2 window.

Channel wise MS1 Copy Number for Precursors

Plotting the MS1 copy numbers for all precursors which were associated with one of the defined channels. The copy numbers are calculated using the signal to noise ratio as described in Derks et al. 2022. By default a resolution of 70,000 is used during preprocessing. It can be changed with the –resolution parameter

Identifications

Number of Confident Precursor Identifications

Plotting the number of precursors identified at each given confidence level.

Precursors by Quantification Strategy

Number of precursors found based on quantification startegy. Ms2 precursors are counted based on Precursor.Quantity > 0 and Ms1 precursors are counted based on Ms1.Area > 0.

Precursors by Modification

Number of precursors found based on modification types specified

## [1] "Plot failed to render. Reason: Error in `[.data.frame`(data()[[\"report\"]], , c(\"Raw.file\", \"Ms1.Area\", : undefined columns selected\n"

Miscleavage Rate (percentage), PEP < 0.01

Miscleavage rate (percentage) for precursors identified with confidence PEP < 0.01

Miscleavage Rate (K), PEP < 0.01

Plotting frequency of lysine miscleavages in confidently identified precursors.

Miscleavage Rate (R), PEP < 0.01

Plotting frequency of arginine miscleavages in confidently identified precursors.

Number of Protein Identifications

Number of proteotypic protein IDs found per run. Protein IDs are shown across all channels in an experiment.

plex-DIA Diagnostics

Identified Precursors per Channel

The number of precursors identified is shown for every channel together with the number of total and intersected precursors. The number of precursors is based on all precursors found in the report.tsv file which is by default controlled by a run-specific FDR.

Identified Precursors per Channel, Channel Q-Value

The number of precursors identified is shown for every channel together with the number of total and intersected precursors. The number of precursors is based on all precursors with a Channel.Q.Value <= 0.01.

Identified Proteins per Channel

The number of Proteins identified is shown for every channel together with the number of total and intersected proteins. The number of proteins is based on all proteotypic precursors independent of the Protein.Q.Value.

Relative Single-Cell Intensity

Single-Cell intensity relative to the carrier channel for intersected precursors

MS1 Quantification Variability

Single-Cell intensity relative to the carrier channel for intersected precursors

MS2 Quantification Variability

Single-Cell intensity relative to the carrier channel for intersected precursors

Total MS1 Precursors

Total number of precursors identified based on different confidence metrics.

## [1] "Plot failed to render. Reason: Error: Upload ms1_extracted.tsv\n"

Missing Data, Precursor Level

Plotting the Jaccard Index for identified precursors for all channel combinations.

Missing Data, Protein Level

Plotting the Jaccard Index for identified precursors for all channel combinations.

Feature Detection

Features Identified by Charge

Identified features are reported based on the charge. Precursors quantified in seperate channels are treated as separate precursors..

Isotopic Peaks Identified per Feature

The number of isotopic peaks identified is shown for features detected in the Dinosaur search.

Number of Scans per feature

The number of MS1 scans is shown for all features identified in the Dinosaur search.

Retention Length of Features at Base

Plotting the retention length of identified features at the base.

Features Identified across Gradient

The frequency of precursor identifications based on the Dinosaur search is plotted across the chromatographic gradient.

Features Identified across m/z

The frequency of precursor identifications based on the Dinosaur search is plotted across the mass to charge ratio.

Feature Intensity Distribution

The distribution of integrated intensities is shown for identified features.